------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/minimap2 XDG_CONFIG_HOME=/construction/biology/minimap2 HOME=/construction/biology/minimap2 TMPDIR="/tmp" PATH=/construction/biology/minimap2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/minimap2 XDG_CONFIG_HOME=/construction/biology/minimap2 HOME=/construction/biology/minimap2 TMPDIR="/tmp" PATH=/construction/biology/minimap2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- CFLAGS+=-Wextra DESTDIR=/construction/biology/minimap2/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/minimap2" EXAMPLESDIR="share/examples/minimap2" DATADIR="share/minimap2" WWWDIR="www/minimap2" ETCDIR="etc/minimap2" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/minimap2 DOCSDIR=/usr/local/share/doc/minimap2 EXAMPLESDIR=/usr/local/share/examples/minimap2 WWWDIR=/usr/local/www/minimap2 ETCDIR=/usr/local/etc/minimap2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> minimap2-2.20 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> minimap2-2.20 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by minimap2-2.20 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> minimap2-2.20 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by minimap2-2.20 for building => SHA256 Checksum OK for lh3-minimap2-v2.20_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> minimap2-2.20 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by minimap2-2.20 for building ===> Extracting for minimap2-2.20 => SHA256 Checksum OK for lh3-minimap2-v2.20_GH0.tar.gz. Extracted Memory Use: 1.03M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for minimap2-2.20 ===> Applying ports patches for minimap2-2.20 from /xports/biology/minimap2/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> minimap2-2.20 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> minimap2-2.20 depends on package: gmake>=4.3 - found ===> Configuring for minimap2-2.20 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for minimap2-2.20 gmake[1]: Entering directory '/construction/biology/minimap2/minimap2-2.20' cc -c -pipe -O2 -fno-strict-aliasing -Wextra main.c -o main.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra kthread.c -o kthread.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra kalloc.c -o kalloc.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra misc.c -o misc.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra bseq.c -o bseq.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra sketch.c -o sketch.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra sdust.c -o sdust.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra options.c -o options.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra index.c -o index.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra lchain.c -o lchain.o lchain.c: In function 'mg_chain_backtrack': lchain.c:41:24: warning: operand of ?: changes signedness from 'int' to 'uint64_t' {aka 'long unsigned int'} due to unsignedness of other operand [-Wsign-compare] sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; ^~~~~~~~~~~~~~~~~~~~~~ lchain.c:53:24: warning: operand of ?: changes signedness from 'int' to 'uint64_t' {aka 'long unsigned int'} due to unsignedness of other operand [-Wsign-compare] sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; ^~~~~~~~~~~~~~~~~~~~~~ lchain.c: In function 'mg_lchain_dp': lchain.c:174:42: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) { ^ lchain.c:188:43: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i])) ^~ index.c: In function 'mm_idx_name2id': index.c:149:25: warning: operand of ?: changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] return k == kh_end(h)? -1 : kh_val(h, k); ^~ lchain.c: In function 'mg_lchain_rmq': lchain.c:279:103: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) { ^ lchain.c:288:134: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) { ^ index.c: In function 'mm_idx_gen': index.c:359:63: warning: operand of ?: changes signedness from 'int' to 'uint64_t' {aka 'long unsigned int'} due to unsignedness of other operand [-Wsign-compare] pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size; ^~~~~~~~~~~~~~~ lchain.c:341:20: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root); ^ index.c: In function 'mm_idx_dump': index.c:460:16: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (i = 0; i < 1<b; ++i) { ^ index.c: In function 'mm_idx_load': index.c:508:16: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (i = 0; i < 1<b; ++i) { ^ index.c: In function 'mm_idx_bed_read': index.c:725:16: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals ^ index.c: In function 'mm_idx_bed_junc': index.c:735:35: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'const unsigned int'} [-Wsign-compare] if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1; ^~ cc -c -pipe -O2 -fno-strict-aliasing -Wextra align.c -o align.o align.c: In function 'mm_get_hplen_back': align.c:346:29: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (mm_seq4_get(mi->S, i) != c) break; ^~ align.c: In function 'mm_seed_ext_score': align.c:533:49: warning: operand of ?: changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] re = re + ext_len < (int32_t)mi->seq[rid].len? re + ext_len : mi->seq[rid].len; ^~~~~~~~~~~~ align.c: In function 'mm_align1': align.c:622:45: warning: operand of ?: changes signedness from 'int32_t' {aka 'int'} to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len; ^~~~~~ align.c:674:44: warning: operand of ?: changes signedness from 'int32_t' {aka 'int'} to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re; ^ cc -c -pipe -O2 -fno-strict-aliasing -Wextra hit.c -o hit.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra seed.c -o seed.o seed.c: In function 'mm_seed_select': seed.c:40:14: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (a[i].n > max_occ) ++m; ^ seed.c:43:24: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (i == n || a[i].n <= max_occ) { ^~ seed.c:46:26: warning: operand of ?: changes signedness from 'int' to 'unsigned int' due to unsignedness of other operand [-Wsign-compare] int32_t pe = i == n? len : (uint32_t)a[i].q_pos>>1; ^~~ seed.c:56:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap ^ seed.c:64:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (a[j].n > max_max_occ) ^ seed.c: In function 'mm_collect_matches': seed.c:83:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (i = 0; i < n_m0; ++i) ^ seed.c:84:15: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (m[i].n > max_occ) ^ seed.c:87:49: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) { ^ cc -c -pipe -O2 -fno-strict-aliasing -Wextra map.c -o map.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra format.c -o format.o map.c: In function 'mm_dust_minier': map.c:53:42: warning: operand of ?: changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'const long unsigned int'} due to unsignedness of other operand [-Wsign-compare] int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32; ^ map.c:54:36: warning: operand of ?: changes signedness from 'int32_t' {aka 'int'} to 'unsigned int' due to unsignedness of other operand [-Wsign-compare] int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v]; ^ format.c: In function 'mm_event_identity': format.c:272:16: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (i = 0; i < r->p->n_cigar; ++i) { ^ In file included from mmpriv.h:4, from format.c:7: format.c: In function 'write_sam_cigar': format.c:382:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] assert(clip_len[0] < qlen && clip_len[1] < qlen); ^ format.c:382:45: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] assert(clip_len[0] < qlen && clip_len[1] < qlen); ^ cc -c -pipe -O2 -fno-strict-aliasing -Wextra pe.c -o pe.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra esterr.c -o esterr.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra splitidx.c -o splitidx.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse2 ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse4.1 -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse4.1 -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse4.1 -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse2 -mno-sse4.1 -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse2 -mno-sse4.1 -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse2 -mno-sse4.1 -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o cc -c -pipe -O2 -fno-strict-aliasing -Wextra -msse4.1 -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o cc -D_SDUST_MAIN -pipe -O2 -fno-strict-aliasing -Wextra sdust.c kalloc.o -o sdust -lz cc -c -pipe -O2 -fno-strict-aliasing -Wextra example.c -o example.o example.c: In function 'main': example.c:49:19: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings! ^ ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') cc -pipe -O2 -fno-strict-aliasing -Wextra main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread cc -pipe -O2 -fno-strict-aliasing -Wextra example.o -o minimap2-lite -L. -lminimap2 -lm -lz -lpthread gmake[1]: Leaving directory '/construction/biology/minimap2/minimap2-2.20' SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for minimap2-2.20 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/minimap2/minimap2-2.20' mkdir -p /construction/biology/minimap2/stage/usr/local/bin mkdir -p /construction/biology/minimap2/stage/usr/local/man/man1 install -c minimap2 /construction/biology/minimap2/stage/usr/local/bin install -c minimap2-lite /construction/biology/minimap2/stage/usr/local/bin install -c sdust /construction/biology/minimap2/stage/usr/local/bin install -c minimap2.1 /construction/biology/minimap2/stage/usr/local/man/man1 strip /construction/biology/minimap2/stage/usr/local/bin/minimap2 strip /construction/biology/minimap2/stage/usr/local/bin/minimap2-lite strip /construction/biology/minimap2/stage/usr/local/bin/sdust gmake[1]: Leaving directory '/construction/biology/minimap2/minimap2-2.20' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for minimap2-2.20 file sizes/checksums [4]: 0% file sizes/checksums [4]: 100% packing files [4]: 0% packing files [4]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:09